Does God's own PR company handle the account for milk? How else has it managed to hang on to its untarnished image, despite gallons of evidence to the contrary? White ergo pure, natural, nutritionally essential: milk seems more an element than a product, as if it were nature in a carton. While the reputation of other animal foodstuffs has plummeted, milk's has stayed relatively buoyant. Indeed, many people believe that their health will be jeopardised if they don't drink it. In the US, milk is virtually the national emblem (apple pie, in comparison, is an also-ran).

Yet something is bubbling up in the milk pan. The animal welfare groups, for so long preoccupied with chicken and beef farming, have begun to take up the cause of the dairy cow. The scientific evidence, too, is massing up that regular consumption of large quantities of milk can be bad for your health, and campaigners are making a noise about the environmental and international costs of large-scale intensive European dairy farming. Will milk be the site on which health scares meet animal rights?

We have been weaned on the idea that cows' milk is the most complete food to serve youngsters - default sustenance for picky children, liquid calcium for thirsty bones. So thorough is our dairy indoctrination that it requires a total gestalt switch to contemplate the notion that milk may help to cause the very diseases it's meant to prevent. Yet as far back as 1974, the Committee on Nutrition of the American Academy of Pediatrics (AAP) was answering the question, "Should milk drinking by children be discouraged?" (even posing it seems heretical) with a "maybe".

Today, there's a big bank of scientific evidence against milk consumption, alleging not only that it causes some diseases but, equally damning, that it fails to prevent others for which it has traditionally been seen as a panacea. At the same time, new claims about its health-enhancing properties are being advanced almost monthly - 30 years on, the AAP has changed its mind and now recommends dairy products for children. For this is a story of evidence and counter-evidence, of an elixir tainted and attempts to restore it to its previous pre-eminence. At stake are enormous commercial interests, deeply rooted patterns of agriculture and consumption - and our health.

It starts in infancy. Frank Oski, former paediatrics director at Johns Hopkins school of medicine, estimated in his book Don't Drink Your Milk! that half of all iron deficiency in US infants results from cows' milk-induced intestinal bleeding - a staggering amount, since more than 15% of American under-twos suffer from iron-deficiency anaemia. The infants, it seems, drink so much milk (which is very low in iron) that they have little appetite left for foods containing iron; at the same time, the milk, by inducing gastrointestinal bleeding, causes iron loss.

The dairy industry acknowledges (as Hippocrates did) that some people are allergic to milk - though this makes it sound as if the problem lies in the individual's aberrant constitution, rather than in the beverage itself. Yet, when you look at it more closely, the extent of lactose intolerance is extraordinary. Lactose is the sugar in milk, and it needs to be broken down by the enzyme lactase that lives in our intestines and bowels. If the lactose we absorb is greater than our lactase capacity, undigested lactose travels to the large intestine, where it ferments, producing gas, carbon dioxide and lactic acid. The result? Bloating, cramps, diarrhoea and farts. In 1965, investigators at Johns Hopkins found that 15% of all the white people and almost three-quarters of all the black people they tested were unable to digest lactose. Milk, it seemed, was a racial issue, and far more people in the world are unable than able to digest lactose. That includes most Thais, Japanese, Arabs and Ashkenazi Jews, and 50% of Indians.

According to various studies, there's a whole catalogue of other illnesses that can be attributed to cows' milk, among them diabetes. A 1992 report in the New England Journal of Medicine corroborated a long-standing theory that proteins in cows' milk can damage the production of insulin in those with a genetic predisposition to diabetes. The dairy industry dismisses this as "just a theory" - along with "myth" and "controversial", a term it applies to almost all studies critical of milk.

The anti-milk lobby also claims that consumption of dairy products can aggravate rheumatoid arthritis and has been implicated in colic, acne, heart disease, asthma, lymphoma, ovarian cancer and multiple sclerosis. Major studies suggesting a link between milk and prostate cancer have been appearing since the 1970s, culminating in findings by the Harvard School of Public Health in 2000 that men who consumed two and a half servings of dairy products a day had a third greater risk of getting prostate cancer than those who ate less than half a serving a day. In the same year, T Colin Campbell, the Jacob Gould Schurman Professor of Nutritional Biochemistry at Cornell University, said that "cows' milk protein may be the single most significant chemical carcinogen to which humans are exposed".

To milk advocates, this is outrageous. They counter that milk actively protects against a whole cluster of diseases, reducing the risk of hypertension and perhaps kidney stones. Milk, they say, helps remineralise tooth enamel and can be positively anticarcinogenic (particularly against colon cancer). What's more, Harvard University's huge Nurses' Health Study found a lower risk of breast cancer in pre- (but not post-) menopausal women who consumed a lot of low-fat dairy foods such as skimmed milk. Even more dramatic is a Norwegian study of premenopausal women that showed those who drank three glasses of milk a day had a 50% - yes, 50% - lower incidence of breast cancer. But stay that hand reaching for a latte: another Norwegian study found that those who drank three-quarters of a litre or more of full-fat milk a day had a significantly greater risk of breast cancer than those who drank more modest amounts. And so it goes.

As with milk and cancer, so with milk and fats: the research is by no means unanimous. Dissenting studies reach quite different conclusions. In one, Scottish men who drank milk every day were found to have a slightly lower risk of heart disease than those who didn't. Similarly, the Honolulu Heart Study found that non milk-drinking men had twice the risk of stroke of those who drank 16oz a day, while the Caerphilly Study found an almost 90% lower risk of heart attacks and strokes among Welshmen who drank at least a pint of full-cream milk a day.

The critics say these are small studies, in which other dietary and genetic factors, exercise and alcohol may swamp the effects of milk drinking. But couldn't the same accusation be levelled at studies revealing the malign consequences of milk? Not so, say the critics: those studies are far larger, build in the countervailing factors and still come up with a strong correlation between the saturated fats in milk and the risk factors for ill health.

Yet even if milk does play a part in causing some diseases, surely it's crucial in avoiding others? "After the first year of life," concluded Oski, "the child requires no milk of any type. The child, like... adults, can thrive without cow milk ever crossing [its] lips." A profane statement such as that lights a flare of questions. What about osteoporosis and our need for calcium? Surely if we don't eat dairy products we'll become brittle-boned and frail, destined for the dowager's hump? It's an intriguing coincidence that just as the alarm was sounding about the fat content of milk products, along came the panic about osteoporosis to propel us straight back to dairy.

To the milk critics, the shibboleth that osteoporosis is caused by calcium deficiency is one of the great myths of our time (each side accuses the other of myth peddling). Mark Hegsted, a retired Harvard professor of nutrition, has said, "To assume that osteoporosis is due to calcium deficiency is like assuming that infection is due to penicillin deficiency." In fact, the bone loss and deteriorating bone tissue that take place in osteoporosis are due not to calcium deficiency but rather to its resorption: it's not that our bodies don't get enough calcium, rather that they excrete too much of what they already have. So we need to find out what it is that's breaking down calcium stores in the first place, to the extent that more than one in three British women now suffers from osteoporosis.

The most important culprit is almost certainly the overconsumption of protein. High-protein foods such as meat, eggs and dairy make excessive demands on the kidneys, which in turn leach calcium from the body. One solution, then, isn't to increase our calcium intake, but to reduce our consumption of protein, so our bones don't have to surrender so much calcium. Astonishingly, according to this newer, more critical view, dairy products almost certainly help to cause, rather than prevent, osteoporosis.

Consider this: American women are among the biggest consumers of calcium in the world, yet still have one of the highest levels of osteoporosis in the world. Lots of researchers have tried to work out the relationship between these two facts. A study funded by the US National Dairy Council, for example, gave a group of postmenopausal women three 8oz glasses of skimmed milk a day for two years, then compared their bones with those of a control group of women not given the milk. The dairy group consumed 1,400mg of calcium a day, yet lost bone at twice the rate of the control group. Similarly, the Harvard Nurses' Health Study found that women who consumed the most calcium from dairy foods broke more bones than those who rarely drank milk. Another piece of research found that women who get most of their protein from animal sources have three times the rate of bone loss and hip fractures of women who get most of their protein from vegetable sources, according to a 2001 National Institutes of Health study.

The pattern of diet and fractures in other parts of the world is equally revealing. Most Chinese people eat and drink no dairy products, and get all their calcium from vegetables. Yet while they consume only half the calcium of Americans, osteoporosis is uncommon in China, despite an average life expectancy of 70. In South Africa, Bantu women who eat mostly plant protein and only 200-350mg of calcium a day have virtually no osteoporosis, despite bearing on average six children and breastfeeding for prolonged periods. Their African-American brothers and sisters, who ingest on average more than 1,000mg of calcium a day, are nine times more likely to experience hip fractures. Campbell puts it unequivocally: "The association between the intake of animal protein and fracture rates appears to be as strong as that between cigarette smoking and lung cancer."

Almost none of these scientific findings has been reflected in mainstream nutritional advice, which continues to emphasise the need for calcium. In fact, the recommendations on calcium are now so high that it is difficult to devise practical diets that meet them. The AAP, for example, currently recommends five daily servings from the milk group for adolescents (try getting those into figure-conscious teenage girls).

But there's another vital part of the calcium puzzle that suggests that the American Dietetic Association and its UK counterparts are looking in the wrong place. Instead of recommending multiple servings of dairy, they'd probably have done better to advise women, and especially teenage girls, to take more exercise. A 15-year study published in the British Medical Journal found that exercise may be the best protection against hip fractures and that "reduced intake of dietary calcium does not seem to be a risk factor". Similarly, researchers at Penn State University concluded that bone density is affected by how much exercise girls get in their teen years, when up to half of their skeletal mass is developed. The girls who took part in this research had wildly different calcium intakes, but it had no lasting effect on their bone health. "We [had] hypothesised that increased calcium intake would result in better adolescent bone gain," said one researcher. "Needless to say, we were surprised to find our hypothesis refuted."

What's the dairy industry's response to all this? The Americans say the idea that excess protein makes you pee out calcium is controversial. The British call it a myth. And those figures on the higher rates of fracture in countries where large amounts of dairy are consumed? Ah, they say, that can be explained by the fact that the northern hemisphere has a limited number of months a year when we're outside for long enough for our bodies to synthesise vitamin D, which is vital for the absorption of calcium. And they're right - vitamin D is critical. In a major follow-up to the Nurses' Health Study, the risk of hip fracture in postmenopausal women was reduced not by milk or a high-calcium diet, but by higher vitamin D intake.

The Dairy Council also says that we protein- and calcium-guzzling northerners keep breaking our hips because of our sedentary lifestyle - ie, we don't exercise enough. Remarkably, here they acknowledge one of the milk critics' central arguments: that no matter how much calcium you down, without adequate exercise and vitamin D, it's to no avail. So much for milk as the great bone protector.

By now, the reader (unless you're Bantu) may be despairing. So what is it that you should be eating, especially since soya milk is now suspected of having undesirable, even toxic, effects. Should we eat nothing, since all of it makes us sick? Or, in that case, we might as well eat everything? For the record, calcium from leafy vegetables seems pretty benign (though watch out for pesticides) - it is, after all, where elephants, rhinos and most other animals get their strong bones from - as are nuts, seeds and dried fruit. Absurd, says the dairy industry: you'd need seven servings of cooked broccoli or eight medium bags of peanuts to get the same amount of calcium as in a 200ml glass of milk. Milk isn't only nutrient-dense, but it needs no preparation and is easily swallowed, both important considerations with the very young and the old.

But given that the benefits of cows' milk have been seriously questioned, why is it still nutritional orthodoxy and a staple of government policy? One reason is history. Even within living memory, rickets was widespread. In the poor living conditions that the working class had to endure early last century, milk seemed indispensable, with the result that it came to be indissolubly linked to health. The 1934 Milk Act, providing elementary schoolchildren with a third of a pint a day at the subsidised price of a halfpenny, enshrined this idea; by 1965, the majority of English and Welsh schoolchildren were downing their daily third. When, in 1971, as minister of education, Margaret Thatcher controversially decided to withdraw free school milk for children over seven, she was widely vilified as a "milk-snatcher". (Perhaps she's retrospectively due some gratitude?)

Yet already 10 years earlier, the Framingham Heart Study had reported a link between coronary heart disease and raised cholesterol levels, and by the 1970s the Royal College of Physicians was recommending the replacement of saturated fats by polyunsaturated. But still the association of milk with health is hard to break. Says Tim Lang, professor of food policy at City University, "The contradictions in policy are a leftover from the 1940s, when nutritionists argued, with justification, that milk provided a good technical fix for poverty. Sixty years on, nutritional science has advanced, and important evidence of the impact of saturated fats has come to the fore."

Another reason why official policy on milk is often at odds with medical evidence lies in the conflict of government role, both in Britain and the US. The US department of agriculture, for example, has the twin, and often mutually incompatible, tasks of promoting agricultural products and providing dietary advice. In 2000, it was still recommending two to three servings of dairy products a day, to the rage of critics such as the Physicians Committee for Responsible Medicine. PCRM claimed that six of the 11-member drafting panel had close ties with the meat, egg and dairy industries (five of them with dairy).

Britain isn't free from conflict of interest, either. The government is heavily involved in encouraging us to drink milk. The department for the environment, food and rural affairs (Defra) sponsors both the dairy industry and the Milk Development Council, responsible for the generic marketing of milk. Equally parti pris are the British and US dairy councils - apparently the source of public health information, but in reality branches of the milk business. In the UK, the National Dairy Council is the promotional arm of the industry, funded by dairy farmers, milk processors and manufacturers. Its website includes the "fact" that eating three portions of dairy products a day significantly lowers cholesterol and the risk of coronary heart disease. Of course, it's no crime for the industry to promote itself; what's disturbing is its masquerading as a disinterested source of incontrovertible information.

What has galvanised the whole debate has been a major change in our dietary habits. We just aren't drinking milk in the quantities we used to. The British went down from 30.55 gallons each a year in 1969 to 25.42 in 1993; by 2001, this had fallen further. But the milk industry is fighting back.